For mass programming you could use a test fixture with pogo pins, using this pins you could force a boot for example form an SD card placed in the test fixture.

This SD card would boot and program your board.

Another solution is to use JTAG to flash the eMMC and blow the fuses. You can contact for example Segger and probably they can adapt their software in order to support your application. Also they have standalone JTAG programmers.